Notes on Engineering Research and Development, Volume 3 Number 2
importance and role of proteins in the human body, followed by a brief description of my project.
Protein structure As mentioned earlier, proteins, upon synthesis, collapse into their native conformations. Biochemists often refer to four distinct aspects of a protein's structure:
Protein basics - What they are and how they're formed Proteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a protein are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
Primary structure: It simply refers to the amino acid sequence. Secondary structures: These are regularly repeating local structures stabilized by hydrogen bonds. The most common examples are the alpha helix, beta sheet and turns. Because secondary structures are local, many regions of different secondary structure can be present in the same protein molecule. Tertiary structure: It refers to the overall shape of a single protein molecule; the spatial relationship of the secondary structures to one another. Tertiary structure is generally stabilized by nonlocal interactions, mostly the formation of a hydrophobic core, but also through salt bridges, hydrogen bonds, disulfide bonds, and e v e n p o s t translational modifications. The term "tertiary structure" is often used as synonymous with the term fold. The tertiary structure is what controls the basic function of the protein. Quaternary structure: It the structure formed by several protein m o l e c u l e s (polypeptide chains), usually called protein subunits in this context, which function as a single protein complex.
DNA molecules have a double helical structure, with molecules called nucleotides on the two strands which are opposite to each other, being paired with one another by hydrogen bonds. This is called complementary pairing, as, of the four nucleotides there are two specific pairs that can bind with each other. Groups of three consecutive nucleotides, called codons code for a specific amino acid, and this codon-amino acid relation is called the genetic code. Thus, the segment of a DNA molecule which codes for a particular protein, and is called a gene, has its nucleotides arranged in the s e q u e n c e corresponding to the amino acid sequence for that particular protein. So, when a cell needs to produce a protein, the gene segment coding for that particular protein, is 'transcripted' into what is known as premessenger RNA, thanks to the complementary pairing property of nucleotides, and this m-RNA then leaves the nucleus, travels to the cytoplasm, and is read by a cell organelle called ribosome to get 'translated' to form the corresponding protein. The protein now travels wherever the cell needs it to be, and performs its functions.
Methods of protein structural prediction Due to the importance of protein structure in determining its function, various bioinformatics tools have been developed to help predict structures of proteins of known amino acid sequence.
Once a protein is synthesized, it collapses into a specific three dimensional structure by a process called protein folding, and this unique shape into which a protein folds is known as its native conformation. Different types of proteins perform a wide range of diverse functions: antibodies defend the body from foreign substances called antigens, contractile proteins are involved in cellular movement, enzymes catalyze biochemical reactions, hormonal proteins perform various bodily activities, and structural proteins provide support, to mention a few! Now you know why they're considered one of the most important molecules in the human body!
The determination of protein amino acid sequences is a lot easier than determination of protein 3D structures. Protein sequencing was earlier done by using many chemical methods, by cleaving off the 'last' amino acid from the protein and carrying out various chemical reactions to test which of the 21 possible amino acids it was. This process was then repeated for the remaining protein and so on, till the protein sequence was fully determined. Today, however, another approach is used to determine protein 21